14-73974642-G-T

Variant names:

• chr14-73974642-G-T
• rs758240
• NM_001249.5:c.784+282C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001249.5(ENTPD5):​c.784+282C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,978 control chromosomes in the GnomAD database, including 24,538 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (24538 hom., cov: 32)
• Consequence: ENTPD5 NM_001249.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 7 publications found

Genes affected

ENTPD5 (HGNC:3367): (ectonucleoside triphosphate diphosphohydrolase 5 (inactive)) The protein encoded by this gene is similar to E-type nucleotidases (NTPases)/ecto-ATPase/apyrases. NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD5 contains 4 apyrase-conserved regions which is characteristic of NTPases. [provided by RefSeq, Jan 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD5	NM_001249.5	c.784+282C>A		intron_variant	Intron 11 of 15	ENST00000334696.11	NP_001240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD5	ENST00000334696.11	c.784+282C>A		intron_variant	Intron 11 of 15	5	NM_001249.5	ENSP00000335246.6
ENTPD5	ENST00000557325.5	c.784+282C>A		intron_variant	Intron 11 of 15	2		ENSP00000451810.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84292 AN: 151858 Hom.: 24537 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.567

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.555 AC: 84313 AN: 151978 Hom.: 24538 Cov.: 32 AF XY: 0.557 AC XY: 41377 AN XY: 74278

African (AFR) AF: 0.397 AC: 16426 AN: 41416

American (AMR) AF: 0.647 AC: 9874 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1400 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2938 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7333 AN: 10572

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42319 AN: 67956

Other (OTH) AF: 0.566 AC: 1197 AN: 2114

Alfa AF: 0.533 Hom.: 2894

Bravo AF: 0.544

Asia WGS AF: 0.469 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs758240; hg19: chr14-74441345;